##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TEKRABber_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TEKRABber.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TEKRABber’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ...Warning: program compiled against libxml 212 using older 211
 NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘TEKRABber/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(messages, collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

appTEKRABber: no visible global function definition for ‘grid_page’
appTEKRABber: no visible global function definition for
  ‘grid_card_text’
appTEKRABber: no visible global function definition for ‘grid_card’
appTEKRABber: no visible global function definition for ‘card_header’
appTEKRABber: no visible global function definition for ‘card_body’
appTEKRABber: no visible global function definition for
  ‘selectizeInput’
appTEKRABber: no visible global function definition for ‘actionButton’
appTEKRABber: no visible global function definition for ‘plotlyOutput’
appTEKRABber: no visible global function definition for ‘plotOutput’
appTEKRABber : server: no visible global function definition for
  ‘renderPlotly’
appTEKRABber : server: no visible global function definition for
  ‘plot_ly’
appTEKRABber : server: no visible global function definition for
  ‘observeEvent’
appTEKRABber : server: no visible global function definition for
  ‘renderPlot’
appTEKRABber : server: no visible global function definition for
  ‘ggplot’
appTEKRABber : server: no visible global function definition for ‘aes’
appTEKRABber : server: no visible binding for global variable ‘gene’
appTEKRABber : server: no visible binding for global variable ‘TE’
appTEKRABber : server: no visible global function definition for
  ‘geom_point’
appTEKRABber : server: no visible global function definition for ‘labs’
appTEKRABber : server: no visible global function definition for
  ‘geom_smooth’
appTEKRABber : server: no visible global function definition for
  ‘theme_bw’
appTEKRABber : server: no visible global function definition for
  ‘ggtitle’
appTEKRABber : server: no visible global function definition for
  ‘ggviolin’
appTEKRABber : server: no visible global function definition for ‘ylab’
appTEKRABber : server: no visible global function definition for ‘xlab’
appTEKRABber : server: no visible global function definition for
  ‘theme’
appTEKRABber: no visible global function definition for ‘shinyApp’
corrOrthologTE: no visible binding for global variable ‘i’
corrOrthologTE: no visible binding for global variable ‘j’
corrOrthologTE: no visible global function definition for ‘cor.test’
orthologScale: no visible global function definition for ‘desc’
orthologScale: no visible binding for global variable
  ‘orthologyConfidence’
orthologScale: no visible binding for global variable ‘refLength’
orthologScale: no visible binding for global variable ‘compareLength’
orthologScale: no visible global function definition for ‘across’
orthologScale: no visible binding for global variable ‘refLen’
orthologScale: no visible binding for global variable ‘compareLen’
prepareRMSK: no visible binding for global variable ‘repEnd’
prepareRMSK: no visible binding for global variable ‘repStart’
prepareRMSK: no visible binding for global variable ‘repName’
prepareRMSK: no visible binding for global variable ‘repClass’
prepareRMSK: no visible binding for global variable ‘rLen’
prepareRMSK: no visible binding for global variable ‘cLen’
Undefined global functions or variables:
  TE across actionButton aes cLen card_body card_header compareLen
  compareLength cor.test desc gene geom_point geom_smooth ggplot
  ggtitle ggviolin grid_card grid_card_text grid_page i j labs
  observeEvent orthologyConfidence plotOutput plot_ly plotlyOutput rLen
  refLen refLength renderPlot renderPlotly repClass repEnd repName
  repStart selectizeInput shinyApp theme theme_bw xlab ylab
Consider adding
  importFrom("stats", "cor.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TEKRABber-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DECorrInputs
> ### Title: Generate all the input files for TEKRABber downstream analysis
> ### Aliases: DECorrInputs
> 
> ### ** Examples
> 
> data(speciesCounts)
> data(hg38_panTro6_rmsk)
> hmGene <- speciesCounts$hmGene
> chimpGene <- speciesCounts$chimpGene
> hmTE <- speciesCounts$hmTE
> chimpTE <- speciesCounts$chimpTE
> 
> ## For demonstration, here we only select 1000 rows to save time
> set.seed(1234)
> hmGeneSample <- hmGene[sample(nrow(hmGene), 1000), ]
> chimpGeneSample <- chimpGene[sample(nrow(chimpGene), 1000), ]
> 
> fetchData <- orthologScale(
+     speciesRef = "hsapiens",
+     speciesCompare = "ptroglodytes",
+     geneCountRef = hmGeneSample,
+     geneCountCompare = chimpGeneSample,
+     teCountRef = hmTE,
+     teCountCompare = chimpTE,
+     rmsk = hg38_panTro6_rmsk,
+     version = 105
+ )
Warning: program compiled against libxml 212 using older 211
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Server returned nothing (no headers, no data) [dec2021.archive.ensembl.org]: Empty reply from server
Backtrace:
    ▆
 1. └─TEKRABber::orthologScale(...)
 2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = version)
 3.     └─biomaRt:::.listMarts(...)
 4.       └─biomaRt:::bmRequest(...)
 5.         └─httr2::req_perform(request)
 6.           └─base::tryCatch(...)
 7.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.                 └─value[[3L]](cond)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  <httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition>
  Error in `httr2::req_perform(req)`: HTTP 500 Internal Server Error.
  Backtrace:
      ▆
   1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:21:5
   2.   └─biomaRt::getLDS(...)
   3.     └─biomaRt:::.submitQueryXML(...)
   4.       └─httr2::req_perform(req)
   5.         └─httr2:::handle_resp(req, resp, error_call = error_call)
   6.           └─httr2:::resp_abort(resp, req, body, call = error_call)
   7.             └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/TEKRABber.Rcheck/00check.log’
for details.